Blender Automatic Weights: Is it grabbing more mesh than it should?
Yes, automatic weights don't always give the desired deformations.  You'll likely have to weight paint things manually to get the exact look you're going for.  I'd set my weight paint mode to 'Add', and set the strength to 1.0, and weight paint the leg bones to 1 -- then normalize everything when you're done.

If you'd like the eyes, teeth and tongue to remain separate mesh objects, you can try putting an armature modifier on those mesh objects too, and weight paint those on the same way you would the rest of your model.